Examples with Origin org.vcell.util.Origin used on opensource projects

Example 31 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class PointSpreadFunctionManagement method importPointSpreadFunction.

public void importPointSpreadFunction() {
    AsynchClientTask[] taskArray = new AsynchClientTask[3];
    // select the desired PSF file
    taskArray[0] = new AsynchClientTask("Select a file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ChoosePSFFile(hashTable);
        }
    };
    // create and save the field data object
    taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Component requesterComponent = parentWindow;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            // the following line of code may modify initialFieldDataName
            // normal file name
            checkNameAvailability(hashTable, false, documentManager, requesterComponent);
            File filePSF = (File) hashTable.get("filePSF");
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            ImageDataset imageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(filePSF.getAbsolutePath(), null);
            Extent extent = imageDataset.getExtent();
            ISize isize = imageDataset.getISize();
            Origin origin = new Origin(0, 0, 0);
            CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
            // save field data
            int NumTimePoints = imageDataset.getImageTimeStamps().length;
            int NumChannels = 1;
            double[][][] pixData = new double[NumTimePoints][NumChannels][];
            for (int i = 0; i < NumTimePoints; i++) {
                // images according to zIndex at specific time points(tIndex)
                short[] originalData = imageDataset.getPixelsZ(0, i);
                double[] doubleData = new double[originalData.length];
                for (int j = 0; j < originalData.length; j++) {
                    doubleData[j] = 0x0000ffff & originalData[j];
                }
                pixData[i][NumChannels - 1] = doubleData;
            }
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            // try {
            // fdos = ClientRequestManager.createFDOSFromImageFile(filePSF, false, null);
            // } catch (DataFormatException ex) {
            // throw new Exception("Cannot read image " + filePSF.getAbsolutePath()+"\n"+ex.getMessage());
            // }
            fdos.owner = documentManager.getUser();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = cartesianMesh;
            fdos.doubleSpecData = pixData;
            fdos.specEDI = null;
            fdos.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
            fdos.times = imageDataset.getImageTimeStamps();
            fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
            fdos.origin = origin;
            fdos.extent = extent;
            fdos.isize = isize;
            ExternalDataIdentifier pSFImageEDI = documentManager.saveFieldData(fdos, initialFieldDataName);
            hashTable.put("pSFImageEDI", pSFImageEDI);
        }
    };
    // create a data symbol for the PSF image saved above as field data
    taskArray[2] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // --- create the data symbols associated with the time series
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            ExternalDataIdentifier pSFImageEDI = (ExternalDataIdentifier) hashTable.get("pSFImageEDI");
            String fluorName = "psf_" + initialFieldDataName;
            DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.POINT_SPREAD_FUNCTION, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), pSFImageEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), 0D);
            simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
        }
    };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(parentWindow, hash, taskArray, false, true, null);
}

Example 32 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class DataSymbolsPanel method addVFrapOriginalImages.

private void addVFrapOriginalImages() {
    // add dataset (normal images) from vFrap
    AsynchClientTask[] taskArray = new AsynchClientTask[5];
    // select the desired vfrap file
    taskArray[0] = ChooseVFrapFile();
    taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File vFrapFile = (File) hashTable.get("vFrapFile");
            Component requesterComponent = DataSymbolsPanel.this;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            // ex  ccc8.vfrap
            String vFrapFileNameExtended = vFrapFile.getName();
            {
                // we want to make sure to reload these strings from the hash later on
                String initialFieldDataName = vFrapFileNameExtended.substring(0, vFrapFileNameExtended.indexOf(".vfrap"));
                // we'll save here the "special" vFrap images (prebleach_avg, ...)
                String mixedFieldDataName = initialFieldDataName + "Mx";
                hashTable.put("initialFieldDataName", initialFieldDataName);
                hashTable.put("mixedFieldDataName", mixedFieldDataName);
            }
            if (vFrapFileNameExtended.indexOf(".vfrap") <= -1) {
                throw new RuntimeException("File extension must be .vfrap");
            }
            // normal images
            checkNameAvailability(hashTable, false, documentManager, requesterComponent);
            // ----- read needed info from Virtual FRAP xml file
            System.out.println("Loading " + vFrapFileNameExtended + " ...");
            String xmlString = XmlUtil.getXMLString(vFrapFile.getAbsolutePath());
            MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
            Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
            // loading frap images
            AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
            hashTable.put("annotatedImages", annotatedImages);
            // loading ROIs for display purposes only (see next task)
            ROI[] rois = xmlReader.getPrimaryROIs(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
            LoadVFrapDisplayRoi(hashTable, annotatedImages, rois);
        // Calendar cal = Calendar.getInstance();
        // SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd_hhmmss");
        // DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
        // DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
        // VFrapXmlHelper vFrapXmlHelper = new VFrapXmlHelper();
        // if(vFrapXmlHelper.isAlreadyImported(vFrapFileName, documentManager)) {
        // throw new RuntimeException("FieldData name already in use.");
        // }
        // //				bioModel.setName(vFrapFileName + "-" + sdf.format(cal.getTime()));
        // bioModel.setName(vFrapFileName);
        // BioModel feedbackModel =  documentManager.save(bioModel, null);
        // BioModelChildSummary  childSummary = BioModelChildSummary.fromDatabaseSerialization(xmlString);
        // BioModelInfo biomodelInfo = new BioModelInfo(feedbackModel.getVersion(), feedbackModel.getVersion().getVersionKey(), childSummary );
        // documentWindow.getTopLevelWindowManager().getRequestManager().openDocument(biomodelInfo, documentWindow.getTopLevelWindowManager(), true);
        }
    };
    // show the images from the vfrap file in an OverlayEditorPanelJAI dialog
    taskArray[2] = new AsynchClientTask("Display images", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            if (initialFieldDataName.equals("")) {
                JOptionPane.showMessageDialog(DataSymbolsPanel.this, "Field Data name " + initialFieldDataName + " already in use.");
                // prevents the rest of tasks below from running
                throw UserCancelException.CANCEL_GENERIC;
            }
            AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
            BufferedImage[] displayROI = (BufferedImage[]) hashTable.get("displayROI");
            if (annotatedImages == null || displayROI == null) {
                return;
            }
            // display the images
            OverlayEditorPanelJAI overlayPanel = new OverlayEditorPanelJAI();
            overlayPanel.setAllowAddROI(false);
            ImageDataset imageDataset = annotatedImages.getImageDataset();
            overlayPanel.setImages(imageDataset, 1, 0, new OverlayEditorPanelJAI.AllPixelValuesRange(1, 200));
            overlayPanel.setAllROICompositeImage(displayROI, OverlayEditorPanelJAI.FRAP_DATA_INIT_PROPERTY);
            int choice = DialogUtils.showComponentOKCancelDialog(DataSymbolsPanel.this, overlayPanel, "vFrap Field Data");
            if (choice != JOptionPane.OK_OPTION) {
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
    };
    // save the timepoints from memory to the database as field data
    taskArray[3] = new AsynchClientTask("Saving time series data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
            DocumentManager dm = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (dm == null) {
                throw new RuntimeException("Not connected to server.");
            }
            User owner = null;
            Version version = simulationContext.getVersion();
            if (version == null) {
                // new document, so the owner is the user
                owner = dm.getUser();
            } else {
                owner = simulationContext.getVersion().getOwner();
            }
            // mesh
            ImageDataset imageDataset = annotatedImages.getImageDataset();
            Extent extent = imageDataset.getExtent();
            ISize isize = imageDataset.getISize();
            Origin origin = new Origin(0, 0, 0);
            CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
            // save field data
            int NumTimePoints = imageDataset.getImageTimeStamps().length;
            int NumChannels = 1;
            double[][][] pixData = new double[NumTimePoints][NumChannels][];
            for (int i = 0; i < NumTimePoints; i++) {
                // images according to zIndex at specific time points(tIndex)
                short[] originalData = imageDataset.getPixelsZ(0, i);
                double[] doubleData = new double[originalData.length];
                for (int j = 0; j < originalData.length; j++) {
                    doubleData[j] = 0x0000ffff & originalData[j];
                }
                pixData[i][NumChannels - 1] = doubleData;
            }
            FieldDataFileOperationSpec timeSeriesFieldDataOpSpec = new FieldDataFileOperationSpec();
            timeSeriesFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
            timeSeriesFieldDataOpSpec.cartesianMesh = cartesianMesh;
            timeSeriesFieldDataOpSpec.doubleSpecData = pixData;
            timeSeriesFieldDataOpSpec.specEDI = null;
            timeSeriesFieldDataOpSpec.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
            timeSeriesFieldDataOpSpec.owner = owner;
            timeSeriesFieldDataOpSpec.times = imageDataset.getImageTimeStamps();
            timeSeriesFieldDataOpSpec.variableTypes = new VariableType[] { VariableType.VOLUME };
            timeSeriesFieldDataOpSpec.origin = origin;
            timeSeriesFieldDataOpSpec.extent = extent;
            timeSeriesFieldDataOpSpec.isize = isize;
            // realignment for the case when first timepoint is not zero
            if (timeSeriesFieldDataOpSpec.times[0] != 0) {
                double shift = timeSeriesFieldDataOpSpec.times[0];
                for (int i = 0; i < NumTimePoints; i++) {
                    timeSeriesFieldDataOpSpec.times[i] -= shift;
                }
            }
            Calendar cal = Calendar.getInstance();
            SimpleDateFormat sdf = new SimpleDateFormat("yyMMMdd_hhmmss");
            String formattedDate = sdf.format(cal.getTime());
            hashTable.put("formattedDate", formattedDate);
            // ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec,
            // initialFieldDataName + "_" + formattedDate);
            ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec, initialFieldDataName);
            hashTable.put("imageDataset", imageDataset);
            hashTable.put("timeSeriesEDI", timeSeriesEDI);
        }
    };
    // create the data symbols for the images saved above and display them in the tree/table
    taskArray[4] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // --- create the data symbols associated with the time series
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            ImageDataset imageDataset = (ImageDataset) hashTable.get("imageDataset");
            ExternalDataIdentifier timeSeriesEDI = (ExternalDataIdentifier) hashTable.get("timeSeriesEDI");
            for (double time : imageDataset.getImageTimeStamps()) {
                // String fluorName = TokenMangler.fixTokenStrict("fluor_"+time+"_");
                // while (simulationContext.getDataContext().getDataSymbol(fluorName)!=null){
                // fluorName = TokenMangler.getNextEnumeratedToken(fluorName);
                // }
                // max time interval we can display is about 11 days
                DecimalFormat df = new DecimalFormat("###000.00");
                // String fluorName = "fluor_" + df.format(time) + "_" + formattedDate;
                String fluorName = "fluor_" + df.format(time).substring(0, df.format(time).indexOf(".")) + "s" + df.format(time).substring(1 + df.format(time).indexOf(".")) + "_" + initialFieldDataName;
                // FieldFunctionArguments fluorFFArgs = new FieldFunctionArguments(timeSeriesEDI.getName(), fluorName, new Expression(time), VariableType.VOLUME);
                DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.VFRAP_TIMEPOINT, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), timeSeriesEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), time);
                simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
            }
        }
    };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(this, hash, taskArray, false, true, null);
// String name = null;
// try {
// getNewDataSymbolPanel().setSymbolName("");
// getNewDataSymbolPanel().setSymbolExpression("vcField(dataset1,var1,0.0,Volume)");
// int newSettings = org.vcell.util.gui.DialogUtils.showComponentOKCancelDialog(this, getNewDataSymbolPanel(), "New DataSymbol");
// if (newSettings == JOptionPane.OK_OPTION) {
// name = getNewDataSymbolPanel().getSymbolName();
// String expression = getNewDataSymbolPanel().getSymbolExpression();
// Expression exp = new Expression(expression);
// FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(null);
// //			DataSymbol ds = new FieldDataSymbol(DataSymbolType.GENERIC_SYMBOL, name, "",
// //					simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
// //					new FieldFunctionArguments(functionInvocations[0]));
// DataSymbol ds = new FieldDataSymbol(name, DataSymbolType.GENERIC_SYMBOL,
// simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD);
// simulationContext.getDataContext().addDataSymbol(ds);
// }
// } catch (java.lang.Throwable ivjExc) {
// DialogUtils.showErrorDialog(this, "Data symbol " + name + " already exists");
// }
}

Example 33 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class ROIMultiPaintManager method sampleAnalyticIntoImage.

private void sampleAnalyticIntoImage(OverlayEditorPanelJAI.ImgSubVolHelper imgSubVolHelper) {
    try {
        Extent extent = (editedGeometryAttributes == null ? originalExtent : editedGeometryAttributes.extent);
        Origin orig = (editedGeometryAttributes == null ? originalOrigin : editedGeometryAttributes.origin);
        int numX = roiComposite[0].getWidth();
        int numY = roiComposite[0].getHeight();
        int numZ = roiComposite.length;
        int dim = (roiComposite.length > 1 ? 1 : 0) + (roiComposite[0].getHeight() > 1 ? 1 : 0) + 1;
        double cX = calcCoord(imgSubVolHelper.getMousePoint().x, numX, orig.getX(), extent.getX());
        double cY = calcCoord(imgSubVolHelper.getMousePoint().y, numY, orig.getY(), extent.getY());
        double cZ = calcCoord(imgSubVolHelper.getZCenter(), numZ, orig.getZ(), extent.getZ());
        Coordinate center = new Coordinate(cX, cY, cZ);
        AnalyticSubVolume tempSV = GeometrySubVolumePanel.createAnalyticSubVolume(overlayEditorPanelJAI, dim, center, "tempSV");
        tempSV.rebind();
        for (int k = 0; k < numZ; k++) {
            double coordZ = calcCoord(k, numZ, orig.getZ(), extent.getZ());
            for (int j = 0; j < numY; j++) {
                double coordY = calcCoord(j, numY, orig.getY(), extent.getY());
                for (int i = 0; i < numX; i++) {
                    double coordX = calcCoord(i, numX, orig.getX(), extent.getX());
                    if (tempSV.isInside(coordX, coordY, coordZ, null)) {
                        ((DataBufferByte) roiComposite[k].getRaster().getDataBuffer()).getData()[j * numX + i] = (byte) (imgSubVolHelper.getCurrentSubVolHandle().getContrastColorIndex());
                    }
                }
            }
        }
    } catch (UserCancelException uce) {
    // ignore
    } catch (Exception e) {
        DialogUtils.showErrorDialog(overlayEditorPanelJAI, e.getClass().getName() + " " + e.getMessage());
    }
}

Example 34 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class RayCaster method createGeometryFromSTL.

public static Geometry createGeometryFromSTL(GeometryThumbnailImageFactory geometryThumbnailImageFactory, SurfaceCollection surfaceCollection, int numSamples) throws ImageException, PropertyVetoException, GeometryException, ExpressionException, IOException {
    Node[] nodes = surfaceCollection.getNodes();
    double minX = Double.MAX_VALUE;
    double maxX = -Double.MAX_VALUE;
    double minY = Double.MAX_VALUE;
    double maxY = -Double.MAX_VALUE;
    double minZ = Double.MAX_VALUE;
    double maxZ = -Double.MAX_VALUE;
    for (Node node : nodes) {
        double nx = node.getX();
        double ny = node.getY();
        double nz = node.getZ();
        minX = Math.min(minX, nx);
        maxX = Math.max(maxX, nx);
        minY = Math.min(minY, ny);
        maxY = Math.max(maxY, ny);
        minZ = Math.min(minZ, nz);
        maxZ = Math.max(maxZ, nz);
    }
    Extent extent = new Extent((maxX - minX) * 1.4, (maxY - minY) * 1.4, (maxZ - minZ) * 1.4);
    Origin origin = new Origin(minX - 0.2 * extent.getX(), minY - 0.2 * extent.getY(), minZ - 0.2 * extent.getZ());
    ISize sampleSize = GeometrySpec.calulateResetSamplingSize(3, extent, numSamples);
    Geometry geometry = createGeometry(geometryThumbnailImageFactory, surfaceCollection, origin, extent, sampleSize);
    return geometry;
}

Example 35 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class GeometrySpec method setOrigin.

/**
 * This method was created by a SmartGuide.
 * @param x double
 * @param y double
 */
public void setOrigin(Origin aOrigin) {
    if (!this.origin.compareEqual(aOrigin)) {
        Origin oldOrigin = this.origin;
        this.origin = aOrigin;
        firePropertyChange("origin", oldOrigin, origin);
    }
    return;
}